Did you try to just rendering out a straight uncompressed AVI? I'm thinking there's an issue with temp files being reassembled into the final piece. When you go the mpeg route, the application writes out a two temp files, one for video and the other audio. Then combines them and that might be where the issue is, and hence it's a codec.
You don't have to render the whole thing, just a small sample for testing, a few seconds. See if going AVI uncompressed, works.